@niagads/igv 0.2.0 → 0.2.1

package/dist/IGVBrowser.js

@@ -1,2 +1,2 @@
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+import{__awaiter as e}from"tslib";import{ALWAYS_ON_TRACKS as r,VariantReferenceTrack as t,FEATURE_SEARCH_URL as i,DEFAULT_FLANK as n}from"./config/_constants.js";import o,{useState as s,useRef as a,useMemo as c,useEffect as l,useLayoutEffect as u}from"react";import{loadTracks as d,clearTrackView as f}from"./utils/browser.js";import{resolveTrackConfigs as m,resolveTrackIds as v}from"./utils/track_config.js";import{Skeleton as g}from"@niagads/ui";import{_genomes as p}from"./config/_igvGenomes.js";import{trackPopover as k}from"./tracks/feature_popovers.js";function h(e){return e.replace(/,/g,"").replace("...","-")}function w(r,t){return e(this,void 0,void 0,function*(){var e,i;const n=[...null!==(e=null==t?void 0:t.tracks)&&void 0!==e?e:[],...null!==(i=null==t?void 0:t.files)&&void 0!==i?i:[]];return yield d(r,n),t.tracks?v(t.tracks):[]})}const y=({genome:d="GRCh38",searchUrl:v=i,locus:y,trackConfig:T,referenceTracks:j=[t],defaultTracks:C,files:L={urls:[],indexed:!0},hideNavigation:S=!1,onBrowserLoad:_,onTrackRemoved:b,onLocusChanged:R})=>{const[x,A]=s(!1),[B,E]=s(null),[U,$]=s(!0),[G,N]=s(null),V=a(null),F=a(!1),O=c(()=>{const e=p.find(e=>e.id===d);return{locus:h(y||"ABCA7"),showAllChromosomes:!1,flanking:n,minimumBases:40,showNavigation:!S,search:{url:v,chromosomeField:"chr"},reference:e,loadDefaultGenomes:!1,genomeList:[e],alwaysOnTracks:[...r,...j?m(T,j).filter(e=>!0!==e.removable).map(e=>e.id):[]]}},[d,y]),q=c(()=>{const e={};let r=j?m(T,j):[];C&&r.push(...m(T,C));const t=new Set;if(e.tracks=r.filter(e=>!t.has(e.id)&&t.add(e.id)),L){const r=Array.from(new Set(L.urls));e.files=r.map(e=>{const r="file_"+e.split("/").pop().replace(/\..+$/,"");return L.indexed?{url:e,indexURL:`${e}.tbi`,name:`USER: ${r}`,id:r}:{url:e,name:`USER: ${r}`,id:r}})}return e},[]);return l(()=>{A(!0)},[]),u(()=>{if(x&&V.current){function r(){return e(this,void 0,void 0,function*(){const{default:e}=yield import("igv/dist/igv.esm");E(e)})}function t(){return e(this,void 0,void 0,function*(){const{default:e}=yield import("./tracks/VariantServiceTrack.js"),{default:r}=yield import("./tracks/VariantPValueTrack.js");B.registerTrackClass("gwas_service",r),B.registerTrackClass("qtl",r),B.registerTrackClass("variant_service",e)})}if(B){const i=V.current;t(),null!=O&&B.createBrowser(i,O).then(function(r){return e(this,void 0,void 0,function*(){r.on("trackclick",k),r.on("trackremoved",function(e){b&&b(e.config.id)}),r.on("locuschange",function(e){if(!F.current){let r=e.map(e=>e.getLocusString()).join("%20");R&&R(r)}}),r.on("trackdrag",()=>{F.current=!0}),r.on("trackdragend",()=>{F.current=!1;let e=r.referenceFrameList.map(e=>e.getLocusString()).join("%20");R&&R(e)}),yield w(r,q),$(!1),N(r),_&&_(r)})})}else r()}},[x,B]),l(()=>{G&&G.search(y)},[y]),l(()=>{!U&&G&&e(void 0,void 0,void 0,function*(){f(G,O.alwaysOnTracks),C&&(m(T,C),yield w(G,q))})},[C,T,U,G]),!x&&U?o.createElement(g,{type:"table"}):o.createElement("div",{ref:V,className:"w-full",id:"genome-browser"})};o.memo(y);export{y as default};
 //# sourceMappingURL=IGVBrowser.js.map

package/dist/IGVBrowser.js.map

@@ -1 +1 @@
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package/dist/IGVBrowserWithSelector.js

@@ -1,2 +1,2 @@
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package/dist/IGVBrowserWithSelector.js.map

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package/dist/config/_constants.js

@@ -1,2 +1,2 @@
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+const e=1e6,i=1e3,r=["ideogram","ruler","sequence","ENSEMBL_GENE"],a="https://api.niagads.org",t=`${a}/genomics/legacy`,n=`${a}/genomics/service/igvbrowser/feature?id=$FEATURE$&flank=1000`,o="https://www.niagads.org/genomics/app",s={name:"ADSP R4 Variants",url:`${t}/service/track/variant`,type:"variant_service",format:"webservice",visibilityWindow:1e5,supportsWholeGenome:!1,queryable:!0,description:"Variants from the Alzheimer's Disease Sequencing Project (ADSP) 36K R4 whole genome sequencing effort - INDELs and SNVs that passed the ADSP biallelic quality control (QC) criteria. Variants are annotated by the ADSP Annotation Pipeline.",id:"ADSP_R4",order:1,infoURL:"/record",removable:!1};export{r as ALWAYS_ON_TRACKS,a as API_ROOT,i as DEFAULT_FLANK,n as FEATURE_SEARCH_URL,o as GENOMICSDB_ROOT,t as LEGACY_API_ROOT,e as QTL_VISIBILITY_WINDOW,s as VariantReferenceTrack};
 //# sourceMappingURL=_constants.js.map

package/dist/config/_constants.js.map

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package/dist/decoders/bedDecoder.js

@@ -1,2 +1,2 @@
-import{capitalize as t,numberFormatter as e}from"./utils.js";import r from"igv/dist/igv.esm";const n=["chr","start","end","name","score","strand","cdStart","cdEnd","color","blockCount","blockSizes","blockStarts"],s=["pvalue","p-value","pval","p_value"],o="target_gene_symbol",a="target_ensembl_id",i="variant_id",c=new Set(["user_input","target_info"]);function l(s,o){const a=o.format.match(/bed(\d{1,2})\+(\d+)/),i=parseInt(a[1]);if(parseInt(a[2]),s.length<3)return;const l=s[0],f=parseInt(s[1]),h=s.length>2?parseInt(s[2]):f+1;if(isNaN(f)||isNaN(h))return new r.DecodeError("Unparsable bed record.");let b=new p(l,f,h);Object.defineProperty(b,"popupData",{configurable:!0,enumerable:!1,get(){const r=function(r){const n=new Set(["row","color","chr","start","end","cdStart","cdEnd","strand","alpha"]),s=[];for(const e in r)if("info"===e)for(const t of Object.keys(r)){const n=r[e][t];n&&s.push({name:u(t),value:n})}else if(!n.has(e)){const n=r[e];s.push({name:t(e),value:n})}let o=`${r.chr}:${e(r.start+1)}-${e(r.end)}`;r.strand&&(o+=` (${r.strand})`);return s.push({name:"Location",value:o}),s}(this);return Object.defineProperty(this,"popupData",{value:r,writable:!1}),r}});const m=Object.create(null);for(let t=0;t<o.columnNames.length;t++){m[String(o.columnNames[t]).toLowerCase()]=t}return i>3&&function(t,e,r){const s={};for(let t=3;t<e;t++){const e=n[t],o=d(e,r[t]);null!==o&&("number"==typeof o&&isNaN(o)||(s[e]=o))}t.setAdditionalAttributes(s)}(b,i,s),function(t,e,r,n,s){const o={};for(let t=r;t<n.length;t++){const r=n[t];if(!s.has(r)){let n=e[t];isNaN(n)||"number"==typeof n||(n*=1),"."===n&&(n=null),o[r]=n}}t.setAdditionalAttributes({info:o})}(b,s,i,o.columnNames,c),b.setP(s,m),b.setTarget(s,m),b.setVariant(s,m),b}function u(t){let e=t.charAt(0).toUpperCase()+t.slice(1).toLowerCase();return e=e.replace(/FDR_/gi,"FDR_").replace(/QC_/gi,"QC_").replace(/qtl_/gi,"QTL_").replace(/_/g," ").replace("non ref","(non ref)"),e}function d(t,e){switch(t){case"name":return"."===e?"":e;case"score":return"."===e?0:Number(e);case"strand":return[".","+","-"].includes(e)?e:null;case"cdStart":case"cdEnd":return parseInt(e);case"color":return"."===e||"0"===e?null:r.IGVColor.createColorString(e);default:return e}}class p{constructor(t,e,r,n=1e3){this.start=e,this.end=r,this.chr=t,this.score=n}setAdditionalAttributes(t){Object.assign(this,t)}removeAttributes(t){for(const e of t)delete this[e]}getAttributeValue(t){const e=t;return this.hasOwnProperty(e)?this[e]:this.info.hasOwnProperty(e)?this.info[e]:null}setVariant(t,e){var r;const n=null!==(r=e[i])&&void 0!==r?r:-1;if(-1===n||!t[n])return;const s=String(t[n]).replace("chr","");this.setAdditionalAttributes({variant:s,record_pk:s}),this.name||this.setAdditionalAttributes({name:t[n]}),this.removeAttributes([i])}setP(t,e){for(const r of s){const n=e[r];if(void 0!==n){const e=parseFloat(t[n]);if(isNaN(e))continue;const s=-1*Math.log10(e);this.setAdditionalAttributes({pvalue:e.toExponential(2),neg_log10_pvalue:s}),this.removeAttributes([r]);break}}}setTarget(t,e){const r=e[o],n=void 0!==r?t[r]:void 0,s=e[a],i=void 0!==s?t[s]:n;this.setAdditionalAttributes({gene_symbol:n,gene_id:i}),this.removeAttributes([a,o])}}export{l as default};
+import{capitalize as t,numberFormatter as e}from"./utils.js";import n from"igv/dist/igv.esm";const r=["chr","start","end","name","score","strand","cdStart","cdEnd","color","blockCount","blockSizes","blockStarts"],s=["pvalue","p-value","pval","p_value"],o="target_gene_symbol",a="target_ensembl_id",i="variant_id",c=new Set(["user_input","target_info"]);function l(s,o){const a=o.format.match(/bed(\d{1,2})\+(\d+)/),i=parseInt(a[1]);if(parseInt(a[2]),s.length<3)return;const l=s[0],f=parseInt(s[1]),h=s.length>2?parseInt(s[2]):f+1;if(isNaN(f)||isNaN(h))return new n.DecodeError("Unparsable bed record.");let b=new p(l,f,h);Object.defineProperty(b,"popupData",{configurable:!0,enumerable:!1,get(){const n=function(n){const r=new Set(["row","color","chr","start","end","cdStart","cdEnd","strand","alpha"]),s=[];for(const e in n)if("info"===e)for(const t of Object.keys(n)){const r=n[e][t];r&&s.push({name:u(t),value:r})}else if(!r.has(e)){const r=n[e];s.push({name:t(e),value:r})}let o=`${n.chr}:${e(n.start+1)}-${e(n.end)}`;n.strand&&(o+=` (${n.strand})`);return s.push({name:"Location",value:o}),s}(this);return Object.defineProperty(this,"popupData",{value:n,writable:!1}),n}});const m=Object.create(null);for(let t=0;t<o.columnNames.length;t++){m[String(o.columnNames[t]).toLowerCase()]=t}return i>3&&function(t,e,n){const s={};for(let t=3;t<e;t++){const e=r[t],o=d(e,n[t]);null!==o&&("number"==typeof o&&isNaN(o)||(s[e]=o))}t.setAdditionalAttributes(s)}(b,i,s),function(t,e,n,r,s){const o={};for(let t=n;t<r.length;t++){const n=r[t];if(!s.has(n)){let r=e[t];isNaN(r)||"number"==typeof r||(r*=1),"."===r&&(r=null),o[n]=r}}t.setAdditionalAttributes({info:o})}(b,s,i,o.columnNames,c),b.setP(s,m),b.setGene(s,m),b.setVariant(s,m),b}function u(t){let e=t.charAt(0).toUpperCase()+t.slice(1).toLowerCase();return e=e.replace(/FDR_/gi,"FDR_").replace(/QC_/gi,"QC_").replace(/qtl_/gi,"QTL_").replace(/_/g," ").replace("non ref","(non ref)"),e}function d(t,e){switch(t){case"name":return"."===e?"":e;case"score":return"."===e?0:Number(e);case"strand":return[".","+","-"].includes(e)?e:null;case"cdStart":case"cdEnd":return parseInt(e);case"color":return"."===e||"0"===e?null:n.IGVColor.createColorString(e);default:return e}}class p{constructor(t,e,n,r=1e3){this.start=e,this.end=n,this.chr=t,this.score=r}setAdditionalAttributes(t){Object.assign(this,t)}removeAttributes(t){for(const e of t)delete this[e]}getAttributeValue(t){const e=t;return this.hasOwnProperty(e)?this[e]:this.info.hasOwnProperty(e)?this.info[e]:null}setVariant(t,e){var n;const r=null!==(n=e[i])&&void 0!==n?n:-1;if(-1===r||!t[r])return;const s=String(t[r]).replace("chr","");this.setAdditionalAttributes({variant:s,record_pk:s}),this.name||this.setAdditionalAttributes({name:t[r]}),this.removeAttributes([i])}setP(t,e){for(const n of s){const r=e[n];if(void 0!==r){const e=parseFloat(t[r]);if(isNaN(e))continue;const s=-1*Math.log10(e);this.setAdditionalAttributes({pvalue:e.toExponential(2),neg_log10_pvalue:s}),this.removeAttributes([n]);break}}}setGene(t,e){const n=e[o],r=void 0!==n?t[n]:void 0,s=e[a],i=void 0!==s?t[s]:r;this.setAdditionalAttributes({gene_symbol:r,gene_id:i}),this.removeAttributes([a,o])}}export{l as default};
 //# sourceMappingURL=bedDecoder.js.map

package/dist/decoders/bedDecoder.js.map

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package/dist/index.d.ts

@@ -23,6 +23,7 @@ interface IGVBrowserTrack {
     maxHeight?: number;
     order?: number;
     color?: string;
+    supportsWholeGenome?: boolean;
     queryable?: boolean;
     metadata?: any;
 }
@@ -55,20 +56,7 @@ interface IGVBrowserWithSelectorProps extends IGVBrowserProps {
 }
 declare function IGVBrowserWithSelector({ selectorTable, trackConfig, defaultTracks, ...restBrowserProps }: IGVBrowserWithSelectorProps): React.JSX.Element;
 
-declare const VariantReferenceTrack: {
-    name: string;
-    url: string;
-    type: string;
-    format: string;
-    visibilityWindow: number;
-    supportsWholeGenome: boolean;
-    queryable: boolean;
-    description: string;
-    id: string;
-    order: number;
-    infoURL: string;
-    removable: boolean;
-};
+declare const VariantReferenceTrack: IGVBrowserTrack;
 
 declare const findTrackConfigs: (config: IGVBrowserTrack[], trackIds: string[]) => IGVBrowserTrack[];
 

package/dist/tracks/VariantPValueTrack.js

@@ -1,2 +1,2 @@
-import{__awaiter as t}from"tslib";import e from"./color_scales/manhattan_colors.js";import i from"igv/dist/igv.esm";class a extends i.TrackBase{constructor(t,e){super(t,e)}init(t){super.init(t),this.useChrColors=!1,this.valueProperty="value",this.height=t.height||100,this.autoscale=t.autoscale,this.background=t.background,this.divider=t.divider||"rgb(225,225,225)",this.dotSize=t.dotSize||3,this.popoverWindow=void 0===t.popoverWindow?1e8:t.popoverWindow,this.maxValue=t.max||100,this.colorScales=t.color?new i.ConstantColorScale(t.color):"qtl"===this.config.type?{"*":new i.GradientColorScale(t.colorScale||{low:10,high:100,lowColor:"rgb(135,206,250)",highColor:"rgb(255,165,0)"})}:{"*":new i.BinnedColorScale(t.colorScale||{thresholds:[.3,3,6,7.3,this.maxValue],colors:["rgb(227,238,249)","rgb(251,170,170)","rgb(245, 12, 12)","rgb(255,166,0)","rgb(20, 186, 59)","rgb(16,151,230)"]})},this.featureSource=i.FeatureSource(t,this.browser.genome),this.type=t.type||"variant",this.infoURL=t.infoURL||void 0}postInit(){return t(this,void 0,void 0,function*(){return"function"==typeof this.featureSource.getHeader&&(this.header=yield this.featureSource.getHeader()),this.header&&this.setTrackProperties(this.header),this.autoscale||(this.dataRange={min:void 0===this.config.min?0:this.config.min,max:this.maxValue}),this})}supportsWholeGenome(){return!1}getFeatures(e,i,a){return t(this,void 0,void 0,function*(){const t=this.visibilityWindow;return this.featureSource.getFeatures({chr:e,start:i,end:a,visibilityWindow:t})})}draw(t){const e=t.features,a=t.context,o=t.pixelWidth,r=t.pixelHeight,s=(this.dataRange.max-this.dataRange.min)/r;this.background&&i.IGVGraphics.fillRect(a,0,0,o,r,{fillStyle:this.background}),i.IGVGraphics.strokeLine(a,0,r-1,o,r-1,{strokeStyle:this.divider});let n=this.getColorScale();if(e){const l=t.bpPerPixel,h=t.bpStart,c=h+o*l+1;let u=null;for(const t of e){const e=t.start;if(e<h)continue;if(e>c)break;let o=t._f?t._f.chr:t.chr;o!=u&&(u=o,this.useChrColors&&(n=this.getColorScale(o)));const d=t.neg_log10_pvalue>this.maxValue&&!this.autoscale?this.maxValue:t.neg_log10_pvalue,g=n.getColor(d),f=Math.round((e-h)/l),p=Math.max(this.dotSize,r-Math.round((d-this.dataRange.min)/s));g&&i.IGVGraphics.setProperties(a,{fillStyle:g,strokeStyle:"black"}),i.IGVGraphics.fillCircle(a,f,p,this.dotSize),t.px=f,t.py=p}}}getColorScale(t=void 0){if(!t)return this.colorScales["*"];if(this.useChrColors){let a=this.colorScales[t];if(!a){const o=e[t]||i.randomColorPalette();a=new i.ConstantColorScale(o),this.colorScales[t]=a}return a}return this.colorScales["*"]}paintAxis(t,e,a){i.IGVGraphics.fillRect(t,0,0,e,a,{fillStyle:"rgb(255, 255, 255)"});const o={font:"normal 10px Arial",textAlign:"right",strokeStyle:"black"},r=(this.dataRange.max-this.dataRange.min)/a;if(this.posteriorProbability){const e=.1;for(let s=this.dataRange.min;s<this.dataRange.max;s+=e){const e=a-Math.round((s-this.dataRange.min)/r);i.IGVGraphics.strokeLine(t,45,e-2,50,e-2,o),i.IGVGraphics.fillText(t,s.toFixed(1),44,e+2,o)}}else{const e=Math.ceil(10*(this.dataRange.max-this.dataRange.min)/a);for(let s=this.dataRange.min;s<this.dataRange.max;s+=e){const e=a-Math.round((s-this.dataRange.min)/r);i.IGVGraphics.strokeLine(t,45,e,50,e,o),i.IGVGraphics.fillText(t,Math.floor(s),44,e+4,o)}}o.textAlign="center",this.posteriorProbability?i.IGVGraphics.fillText(t,"PPA",e/2,a/2,o,{rotate:{angle:-90}}):i.IGVGraphics.fillText(t,"-log10(pvalue)",e/2,a/2,o,{rotate:{angle:-90}})}popupData(t,e){const i=this.clickedFeatures(t,e),a=[];if(i){let e=0;for(const o of i){const i=Math.abs(t.canvasX-o.px),r=Math.abs(t.canvasY-o.py);if(i<this.dotSize&&r<this.dotSize){if(e>0&&a.push("<HR/>"),5==e){a.push("...");break}const t=o.end;if(a.push({name:"Location:",value:`${o.chr}:${t}`}),a.push({name:"p-Value:",value:o.pvalue}),this.infoURL){const t=`${this.infoURL}/variant/${o.record_pk}`;a.push({name:"Variant:",html:`<a target="_blank" href="${t}">${o.variant}</a>`,title:`Learn more about variant: ${o.variant}`})}else a.push({name:"Variant",value:o.variant});if("gene_id"in o){const t="gene_symbol"in o?o.gene_symbol:o.gene_id;if(this.infoURL){const e=`${this.infoURL}/gene/${o.gene_id}`;a.push({name:"Target",html:`<a target="_blank" href="${e}">${t}</a>`,title:`Learn more about gene: ${t}`})}else a.push({name:"Target",value:t})}"info"in o&&("qtl_dist_to_target"in o.info&&a.push({name:"Dist. to Target",value:null===o.info.qtl_dist_to_target?"Not reported":o.info.qtl_dist_to_target}),"z_score_non_ref"in o.info&&a.push({name:"Z-score",value:null===o.info.z_score_non_ref?"Not reported":Number(o.info.z_score_non_ref).toFixed(2)})),e++}}}return a}menuItemList(){return this.numericDataMenuItems()}doAutoscale(t){if(t.length>0){const e=t.map(function(t){return{value:t.neg_log10_pvalue}});return i.doAutoscale(e)}return{min:this.config.min||0,max:this.maxValue}}}export{a as default};
+import{__awaiter as t}from"tslib";import e from"./color_scales/manhattan_colors.js";import i from"igv/dist/igv.esm";class a extends i.TrackBase{constructor(t,e){super(t,e)}init(t){super.init(t),this.useChrColors=!1,this.valueProperty="value",this.height=t.height||100,this.autoscale=t.autoscale,this.background=t.background,this.divider=t.divider||"rgb(225,225,225)",this.dotSize=t.dotSize||3,this.popoverWindow=void 0===t.popoverWindow?1e8:t.popoverWindow,this.maxValue=t.max||100,this.visibilityWindow=t.visibilityWindow,this.colorScales=t.color?new i.ConstantColorScale(t.color):"qtl"===this.config.type?{"*":new i.GradientColorScale(t.colorScale||{low:10,high:100,lowColor:"rgb(135,206,250)",highColor:"rgb(255,165,0)"})}:{"*":new i.BinnedColorScale(t.colorScale||{thresholds:[.3,3,6,7.3,this.maxValue],colors:["rgb(227,238,249)","rgb(251,170,170)","rgb(245, 12, 12)","rgb(255,166,0)","rgb(20, 186, 59)","rgb(16,151,230)"]})},this.featureSource=i.FeatureSource(t,this.browser.genome),this.type=t.type||"variant",this.infoURL=t.infoURL||void 0}postInit(){return t(this,void 0,void 0,function*(){return"function"==typeof this.featureSource.getHeader&&(this.header=yield this.featureSource.getHeader()),this.header&&this.setTrackProperties(this.header),this.autoscale||(this.dataRange={min:void 0===this.config.min?0:this.config.min,max:this.maxValue}),this})}supportsWholeGenome(){return!1}getFeatures(e,i,a){return t(this,void 0,void 0,function*(){const t=this.visibilityWindow;return this.featureSource.getFeatures({chr:e,start:i,end:a,visibilityWindow:t})})}draw(t){const e=t.features,a=t.context,o=t.pixelWidth,r=t.pixelHeight,s=(this.dataRange.max-this.dataRange.min)/r;this.background&&i.IGVGraphics.fillRect(a,0,0,o,r,{fillStyle:this.background}),i.IGVGraphics.strokeLine(a,0,r-1,o,r-1,{strokeStyle:this.divider});let n=this.getColorScale();if(e){const l=t.bpPerPixel,h=t.bpStart,c=h+o*l+1;let u=null;for(const t of e){const e=t.start;if(e<h)continue;if(e>c)break;let o=t._f?t._f.chr:t.chr;o!=u&&(u=o,this.useChrColors&&(n=this.getColorScale(o)));const d=t.neg_log10_pvalue>this.maxValue&&!this.autoscale?this.maxValue:t.neg_log10_pvalue,g=n.getColor(d),f=Math.round((e-h)/l),p=Math.max(this.dotSize,r-Math.round((d-this.dataRange.min)/s));g&&i.IGVGraphics.setProperties(a,{fillStyle:g,strokeStyle:"black"}),i.IGVGraphics.fillCircle(a,f,p,this.dotSize),t.px=f,t.py=p}}}getColorScale(t=void 0){if(!t)return this.colorScales["*"];if(this.useChrColors){let a=this.colorScales[t];if(!a){const o=e[t]||i.randomColorPalette();a=new i.ConstantColorScale(o),this.colorScales[t]=a}return a}return this.colorScales["*"]}paintAxis(t,e,a){i.IGVGraphics.fillRect(t,0,0,e,a,{fillStyle:"rgb(255, 255, 255)"});const o={font:"normal 10px Arial",textAlign:"right",strokeStyle:"black"},r=(this.dataRange.max-this.dataRange.min)/a;if(this.posteriorProbability){const e=.1;for(let s=this.dataRange.min;s<this.dataRange.max;s+=e){const e=a-Math.round((s-this.dataRange.min)/r);i.IGVGraphics.strokeLine(t,45,e-2,50,e-2,o),i.IGVGraphics.fillText(t,s.toFixed(1),44,e+2,o)}}else{const e=Math.ceil(10*(this.dataRange.max-this.dataRange.min)/a);for(let s=this.dataRange.min;s<this.dataRange.max;s+=e){const e=a-Math.round((s-this.dataRange.min)/r);i.IGVGraphics.strokeLine(t,45,e,50,e,o),i.IGVGraphics.fillText(t,Math.floor(s),44,e+4,o)}}o.textAlign="center",this.posteriorProbability?i.IGVGraphics.fillText(t,"PPA",e/2,a/2,o,{rotate:{angle:-90}}):i.IGVGraphics.fillText(t,"-log10(pvalue)",e/2,a/2,o,{rotate:{angle:-90}})}popupData(t,e){const i=this.clickedFeatures(t,e),a=[];if(i){let e=0;for(const o of i){const i=Math.abs(t.canvasX-o.px),r=Math.abs(t.canvasY-o.py);if(i<this.dotSize&&r<this.dotSize){if(e>0&&a.push("<HR/>"),5==e){a.push("...");break}const t=o.end;if(a.push({name:"Location:",value:`${o.chr}:${t}`}),a.push({name:"p-Value:",value:o.pvalue}),this.infoURL){const t=`${this.infoURL}/variant/${o.record_pk}`;a.push({name:"Variant:",html:`<a target="_blank" href="${t}">${o.variant}</a>`,title:`Learn more about variant: ${o.variant}`})}else a.push({name:"Variant",value:o.variant});if("gene_id"in o){const t="gene_symbol"in o?o.gene_symbol:o.gene_id;if(this.infoURL){const e=`${this.infoURL}/gene/${o.gene_id}`;a.push({name:"Gene",html:`<a target="_blank" href="${e}">${t}</a>`,title:`Learn more about gene: ${t}`})}else a.push({name:"Gene",value:t})}"info"in o&&("target"in o.info&&a.push({name:"Target",value:o.info.target}),"qtl_dist_to_target"in o.info&&a.push({name:"Dist. to Target",value:null===o.info.qtl_dist_to_target?"Not reported":o.info.qtl_dist_to_target}),"z_score_non_ref"in o.info&&a.push({name:"Z-score",value:null===o.info.z_score_non_ref?"Not reported":Number(o.info.z_score_non_ref).toFixed(2)})),e++}}}return a}menuItemList(){return this.numericDataMenuItems()}doAutoscale(t){if(t.length>0){const e=t.map(function(t){return{value:t.neg_log10_pvalue}});return i.doAutoscale(e)}return{min:this.config.min||0,max:this.maxValue}}}export{a as default};
 //# sourceMappingURL=VariantPValueTrack.js.map

package/dist/tracks/VariantPValueTrack.js.map

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package/dist/tracks/VariantServiceTrack.js

@@ -1,2 +1,2 @@
-import{__awaiter as e}from"tslib";import t from"jquery";import i from"igv/dist/igv.esm";const s="impact",a=[{field:"type",label:"Variant Type",default:"SNV"},{field:"filter",label:"CADD Score",default:"Not reported"},{field:"is_adsp_variant",label:"ADSP Variant",default:"No"},{field:"impact",label:"Consequence Severity",default:"NONE"},{field:"consequence",label:"Consequence Type",default:"other / no predicted consequence"},{field:"is_coding",label:"Coding Variant",default:"No"}];class o extends i.TrackBase{constructor(e,t){e.hasOwnProperty("description")&&(e.hasOwnProperty("metadata")?e.metadata=Object.assign(e.metadata,{Descripton:e.description}):e.metadata={Description:e.description},delete e.description),super(e,t)}init(e){super.init(e),this.visibilityWindow=e.visibilityWindow,this.displayMode=e.displayMode||"EXPANDED",this.labelDisplayMode=e.labelDisplayMode,this.expandedVariantHeight=e.expandedVariantHeight||e.variantHeight||10,this.squishedVariantHeight=e.squishedVariantHeight||2,this.squishedCallHeight=e.squishedCallHeight||1,this.expandedCallHeight=e.expandedCallHeight||10,this.expandedVGap=void 0!==e.expandedVGap?e.expandedVGap:2,this.squishedVGap=void 0!==e.squishedVGap?e.squishedVGap:1,this.expandedGroupGap=e.expandedGroupGap||10,this.squishedGroupGap=e.squishedGroupGap||5,this.featureHeight=e.featureHeight||14,this.visibilityWindow=e.visibilityWindow,this.featureSource=i.FeatureSource(e,this.browser.genome),this.noGenotypeColor=e.noGenotypeColor||"rgb(200,180,180)",this.noCallColor=e.noCallColor||"rgb(225, 225, 225)",this.nonRefColor=e.nonRefColor||"rgb(200, 200, 215)",this.mixedColor=e.mixedColor||"rgb(200, 220, 200)",this.homrefColor=e.homrefColor||"rgb(200, 200, 200)",this.homvarColor=e.homvarColor||"rgb(17,248,254)",this.hetvarColor=e.hetvarColor||"rgb(34,12,253)",this.sortDirection="ASC",this.type=e.type||"variant",this.infoURL=e.infoURL||void 0,this.colorBy=void 0===e.colorBy?s:e.colorBy,this._initColorBy=void 0===e.colorBy?s:e.colorBy,e.colorTable&&(this.colorTables=new Map,this.colorTables.set(e.colorBy,new i.ColorTable(e.colorTable))),this._color=e.color,this.showGenotypes=void 0===e.showGenotypes||e.showGenotypes,this.variantRowCount(1)}postInit(){return e(this,void 0,void 0,function*(){return this.header=yield this.getHeader(),"dbSNP"===this.config.id?(this.visibilityWindow=1e5,this.displayMode="SQUISHED"):void 0===this.visibilityWindow&&!1!==this.config.indexed&&("function"==typeof this.featureSource.defaultVisibilityWindow?this.visibilityWindow=yield this.featureSource.defaultVisibilityWindow():this.visibilityWindow=1e6),this})}supportsWholeGenome(){return!1}get color(){return this._color}set color(e){this._color=e,this.colorBy=void 0}getHeader(){return e(this,void 0,void 0,function*(){if(!this.header){if("function"==typeof this.featureSource.getHeader){const e=yield this.featureSource.getHeader();e&&(this.callSets=e.callSets||[]),this.header=e}this.sampleNames=this.callSets?this.callSets.map(e=>e.name):[]}return this.header})}getCallsetsLength(){return this.callSets?this.callSets.length:0}getFeatures(t,i,s,a){return e(this,void 0,void 0,function*(){return void 0===this.header&&(this.header=yield this.getHeader()),this.featureSource.getFeatures({chr:t,start:i,end:s,bpPerPixel:a,visibilityWindow:this.visibilityWindow})})}hasSamples(){return this.getCallsetsLength()>0}getSamples(){return{yOffset:this.sampleYOffset,names:this.sampleNames,height:this.sampleHeight}}computePixelHeight(e){if(!e||0==e.length)return 10;const t="COLLAPSED"===this.displayMode?1:this.nVariantRows,i="SQUISHED"===this.displayMode?this.squishedVGap:this.expandedVGap,s="SQUISHED"===this.displayMode?this.squishedVariantHeight:this.expandedVariantHeight,a="SQUISHED"===this.displayMode?this.squishedCallHeight:this.expandedCallHeight;return 10+t*(s+i)+i+((!1===this.showGenotypes?0:this.getCallsetsLength()*t)+1)*(a+i)}variantRowCount(e){this.nVariantRows=e}draw(e){const{context:t,pixelWidth:s,pixelHeight:a,bpPerPixel:o,bpStart:l,pixelTop:r,features:n}=e;i.IGVGraphics.fillRect(t,0,r,s,a,{fillStyle:"rgb(255, 255, 255)"});const h="SQUISHED"===this.displayMode?this.squishedVGap:this.expandedVGap,c="COLLAPSED"===this.displayMode?1:this.nVariantRows,d="SQUISHED"===this.displayMode?this.squishedVariantHeight:this.expandedVariantHeight;this.variantBandHeight=10+c*(d+h);const p=this.callSets,u=this.getCallsetsLength();if(p&&u>0&&!1!==this.showGenotypes&&i.IGVGraphics.strokeLine(t,0,this.variantBandHeight,s,this.variantBandHeight,{strokeStyle:"rgb(224,224,224) "}),n){const e="SQUISHED"===this.displayMode?this.squishedCallHeight:this.expandedCallHeight,a="SQUISHED"===this.displayMode?this.squishedVGap:this.expandedVGap,r=l+s*o+1;for(const s of n){if(s.end<l)continue;if(s.start>r)break;const n="SQUISHED"===this.displayMode?this.squishedVariantHeight:this.expandedVariantHeight,h=10+("COLLAPSED"===this.displayMode?0:s.row*(n+a)),c=n;let d=Math.round((s.start-l)/o);const f=Math.round((s.end-l)/o);let g=Math.max(1,f-d);if(g<3?(g=3,d-=1):g>5&&(d+=1,g-=2),i.IGVGraphics.fillRect(t,d,h,g,c,{fillStyle:this.getVariantColor(s)}),s.pixelRect={x:d,y:h,w:g,h:c},u>0&&!1!==this.showGenotypes){const o="COLLAPSED"===this.displayMode?1:this.nVariantRows;this.sampleYOffset=this.variantBandHeight+a,this.sampleHeight=o*(e+a);let l=0;for(const o of p){const r=s.calls[o.id];if(r){const n="COLLAPSED"===this.displayMode?0:s.row,h=this.sampleYOffset+l*this.sampleHeight+n*(e+a);let c,p=!0,u=!0,f=!1;if(r.genotype)for(const e of r.genotype){if("."===e){f=!0;break}0!==e&&(u=!1),0===e&&(p=!1)}c=r.genotype?f?this.noCallColor:u?this.homrefColor:p?this.homvarColor:this.hetvarColor:this.noGenotypeColor,i.IGVGraphics.fillRect(t,d,h,g,e,{fillStyle:c}),o.pixelRect={x:d,y:h,w:g,h:e}}l++}}}}else console.log("No feature list")}getConsequenceValue(e){const t=e.replace(/ /g,"_");return t.includes(",")?t.split(",")[0]:t}getVariantClass(e,t){if(t.includes("dup"))return"DUP";const i=t.includes("ins"),s=t.includes("del");return i&&s?"INDEL":i?"INS":s?"DEL":e}getColorByValue(e){var t,i,s;switch(this.colorBy){case"type":return this.getVariantClass(e.variant_class_abbrev,e.display_allele);case"is_adsp_variant":return e.is_adsp_variant;case"impact":return null!==e.most_severe_consequence?null===(t=e.most_severe_consequence)||void 0===t?void 0:t.impact:"*";case"consequence":return null!==e.most_severe_consequence?this.getConsequenceValue(null===(i=e.most_severe_consequence)||void 0===i?void 0:i.conseq):"*";case"is_coding":return null!==e.most_severe_consequence?null===(s=e.most_severe_consequence)||void 0===s?void 0:s.is_coding:"*";default:return"*"}}getFilterValue(e){return"."===e||null===e?0:parseFloat(e)}getVariantColor(e){const t=e._f||e;let i;if(this.colorBy){const e="filter"===this.colorBy?this.getFilterValue(t.filter):this.getColorByValue(t.info);i=this.getVariantColorTable(this.colorBy).getColor(e),i||(i="gray")}else i=this._color?"function"==typeof this._color?this._color(t):this._color:"NONVARIANT"===t.type?this.nonRefColor:"MIXED"===t.type?this.mixedColor:this.defaultColor;return i}clickedFeatures(e,t){let i=super.clickedFeatures(e,t);const s="EXPANDED"===this.displayMode?this.expandedVGap:this.squishedVGap,a=s+("SQUISHED"===this.displayMode?this.squishedCallHeight:this.expandedCallHeight),o=e.y;if(o<=this.variantBandHeight){const e="SQUISHED"===this.displayMode?this.squishedVariantHeight:this.expandedVariantHeight,t=Math.floor((o-10)/(e+s));i=i.filter(e=>e.row===t)}else if(this.callSets){const e=this.callSets,t=o-this.variantBandHeight,s=Math.floor(t/this.sampleHeight);if(s>=0&&s<e.length){const o=Math.floor((t-s*this.sampleHeight)/a),l=i.filter(e=>e.row===o),r=e[s];i=l.map(e=>{const t=e.calls[r.id];return function(e,t){if(e.genotype){let i="";if("."===t.alternateBases)i="No Call";else{const s=t.alternateBases.split(",");for(const a of e.genotype)if(i.length>0&&(i+="|"),"."===a)i+=".";else if(0===a)i+=t.referenceBases;else{i+=s[a-1].replace("<","&lt;")}}e.genotypeName=i}}(t,e),t})}}return i}popupData(e,t){const i=this.clickedFeatures(e,t),s=e.genomicLocation,a=this.browser.genome.id,o=this.browser.sampleInformation,l=[];for(const e of i){const t=e._f||e;if(l.length>1&&l.push({html:"<hr/>"}),"function"==typeof t.popupData){const e=t.popupData(s,a);Array.prototype.push.apply(l,e)}else{const e=t;if(void 0!==e.callSetName&&l.push({name:"Name",value:e.callSetName}),e.genotypeName&&l.push({name:"Genotype",value:e.genotypeName}),void 0!==e.phaseset&&l.push({name:"Phase set",value:e.phaseset}),void 0!==e.genotypeLikelihood&&l.push({name:"genotypeLikelihood",value:e.genotypeLikelihood.toString()}),o){const t=o.getAttributes(e.callSetName);t&&Object.keys(t).forEach(function(e){let i=e.replace(/([A-Z])/g," $1");i=i.charAt(0).toUpperCase()+i.slice(1),l.push({name:i,value:t[e]})})}const i=this.getVariantColor(e);if(this.infoURL){const t=this.infoURL+"/variant/"+e.id;l.push({name:"Variant:",html:`<a target="_blank" href="${t}">${e.info.display_id}</a>`,title:"Learn more about this variant: "+e.info.display_id})}else l.push({name:"Variant:",value:e.info.display_id});if(null!==e.info.ref_snp_id&&l.push({name:"Ref SNP ID:",value:e.info.ref_snp_id}),l.push({name:"Location:",value:e.chr+":"+e.info.location}),l.push({name:"Allele:",value:e.info.display_allele}),"type"===this.colorBy?l.push({name:"Class:",value:this.getVariantClass(e.info.variant_class_abbrev,e.info.display_allele),color:i}):l.push({name:"Class:",value:this.getVariantClass(e.info.variant_class_abbrev,e.info.display_allele)}),"is_adsp_variant"===this.colorBy?l.push({name:"ADSP Variant?",value:null===e.info.is_adsp_variant?"No":"Yes",color:i}):l.push({name:"ADSP Variant?",value:null===e.info.is_adsp_variant?"No":"Yes"}),this.getFilterValue(e.filter)>0&&("filter"===this.colorBy?l.push({name:"CADD (PHRED):",value:e.filter,color:i}):l.push({name:"CADD (PHRED):",value:e.filter})),null!==e.info.most_severe_consequence){const t=e.info.most_severe_consequence;if("consequence"===this.colorBy?l.push({name:"Consequence:",value:t.conseq,color:i}):l.push({name:"Consequence:",value:t.conseq}),"impact"===this.colorBy?l.push({name:"Impact:",value:t.impact,color:i}):l.push({name:"Impact:",value:t.impact}),"is_coding"===this.colorBy?l.push({name:"Is Coding?",value:null===t.is_coding?"No":t.is_coding?"Yes":"No",color:i}):l.push({name:"Is Coding?",value:null===t.is_coding?"No":t.is_coding?"Yes":"No"}),null!==t.impacted_gene)if(this.infoURL){const e=this.infoURL+"/gene/"+t.impacted_gene;l.push({name:"Impacted Gene:",html:`<a target="_blank" href="${e}">${t.impacted_gene_symbol}</a>`,title:"Learn more about gene: "+t.impacted_gene_symbol})}else l.push({name:"Impacted Gene:",value:t.impacted_gene_symbol})}}}return l}menuItemList(){const e=[];e.push("<hr/>");const s=t('<div class="igv-track-menu-category igv-track-menu-border-top">');s.text("Color by:"),e.push({name:void 0,object:s,click:void 0,init:void 0}),a.forEach(t=>{const i=this.colorBy===t.field;"is_adsp_variant"===t.field&&this.config.id.includes("ADSP")||e.push(this.colorByCB({key:t.field,label:t.label},i))}),e.push(this.colorByCB({key:void 0,label:"None"},void 0===this.colorBy)),e.push("<hr/>"),this.getCallsetsLength()>0&&(e.push({object:t('<div class="igv-track-menu-border-top">')}),e.push({object:t(i.createCheckbox("Show Genotypes",this.showGenotypes)),click:()=>{this.showGenotypes=!this.showGenotypes,this.trackView.checkContentHeight(),this.trackView.repaintViews()}})),e.push({object:t('<div class="igv-track-menu-border-top">')});const o={COLLAPSED:"Collapse",SQUISHED:"Squish",EXPANDED:"Expand"};for(const s of Object.keys(o))e.push({object:t(i.createCheckbox(o[s],s===this.displayMode)),click:()=>{this.displayMode=s,this.trackView.checkContentHeight(),this.trackView.repaintViews()}});return this.browser.circularView&&!0===this.browser.circularViewVisible&&(e.push("<hr>"),e.push({label:"Add SVs to circular view",click:()=>{const e=[];for(const t of this.trackView.viewports){const i=t.referenceFrame;for(const s of t.getCachedFeatures())s.end>=i.start&&s.start<=i.end&&e.push(s)}const t=i.makeVCFChords(e),s=i.IGVColor.addAlpha(this._color||this.defaultColor,.5);this.browser.circularView.addChords(t,{track:this.name,color:s})}})),e}contextMenuItemList(e){if(this.browser.circularView&&!0===this.browser.circularViewVisible){const t=e.viewport,s=[];return s.push({label:"Add SVs to Circular View",click:()=>{const e=t.referenceFrame,s="all"===e.chr?this.featureSource.getAllFeatures():this.featureSource.featureCache.queryFeatures(e.chr,e.start,e.end),a=i.makeVCFChords(s),o=i.IGVColor.addAlpha(this._color||this.defaultColor,.5);this.browser.circularView.addChords(a,{track:this.name,color:o})}}),s.push("<hr/>"),s}}description(){const e=(e,t)=>`<div class="igv-track-label-popup-shim"><b>${e}: </b>${t}</div>`,t=(e,t)=>`<div class="igv-track-label-popup-shim"><i class="fa fa-square" style="color:${t}"></i> ${e}</div>`;let i='<div class="igv-track-label-popup">';if(i+=e("Track",this.name),this.config&&this.config.metadata)for(const t of Object.keys(this.config.metadata)){i+=e(t,this.config.metadata[t])}if(i+="</div>",this.colorBy){i+='<hr><div class="igv-track-label-popup">';const s=a.filter(e=>e.field==this.colorBy)[0];if(i+=e("Legend",s.label),i+="<br>","filter"===this.colorBy){const e=this.getVariantColorTable(this.colorBy);for(const[s,a]of e.colors.entries()){const o=e.thresholds[s];i+=t(0===o?"N/A":o,a)}}else{const e=this.getVariantColorTable(this.colorBy).colorTable;for(const[a,o]of Object.entries(e))i+=t(a.includes("*")?s.default:"true"===a?"Yes":a.replace("_"," "),o)}i+="</div>"}return i}colorByCB(e,s){return{name:void 0,object:t(i.createCheckbox(e.label,s)),click:()=>{e.key===this.colorBy?(this.colorBy=void 0,delete this.config.colorBy,this.trackView.repaintViews()):(this.colorBy=e.key,this.config.colorBy=e.key,this.trackView.repaintViews())},init:void 0}}getState(){const e=super.getState();return this._color&&"function"!=typeof this._color&&(e.color=this._color),e}getVariantColorTable(e){if(this.colorTables||(this.colorTables=new Map),!this.colorTables.has(e)){let t;switch(e){case"type":t=r;break;case"consequence":t=c;break;case"is_adsp_variant":case"is_coding":t=h;break;case"impact":t=n;break;case"filter":t=l;break;default:t=new i.PaletteColorTable("Set1")}this.colorTables.set(e,t)}return this.colorTables.get(e)}}const l=new i.BinnedColorScale({thresholds:[0,1,10,20,30,40,50],colors:["#45515c","#440d53","#443983","#32678d","#23908c","#37b779","#8fd744"]}),r=new i.ColorTable({DEL:"#ff2101",INS:"#f59300",DUP:"#028401",INV:"#008688",CNV:"#8931ff",INDEL:"#891100","*":"#45515c"}),n=new i.ColorTable({HIGH:"#ff00ff",MODERATE:"#f59300",LOW:"#008000",MODIFIER:"#377eb8","*":"#45515c"}),h=new i.ColorTable({true:"#e41a1c","*":"#45515c"}),c=new i.ColorTable({splice_acceptor_variant:i.appleCrayonPalette.salmon,start_lost:i.appleCrayonPalette.honeydew,splice_region_variant:i.appleCrayonPalette.fern,prime_UTR_variant:i.appleCrayonPalette.clover,splice_donor_variant:i.appleCrayonPalette.moss,inframe_insertion:i.appleCrayonPalette.teal,splice_donor_region_variant:i.appleCrayonPalette.midnight,non_coding_transcript_exon_variant:i.appleCrayonPalette.eggplant,stop_gained:i.appleCrayonPalette.plum,inframe_deletion:i.appleCrayonPalette.maroon,stop_retained_variant:i.appleCrayonPalette.aqua,intron_variant:i.appleCrayonPalette.mocha,missense_variant:i.appleCrayonPalette.maraschino,synonymous_variant:i.appleCrayonPalette.tangerine,intergenic_variant:i.appleCrayonPalette.ocean,frameshift_variant:i.appleCrayonPalette.bubblegum,protein_altering_variant:i.appleCrayonPalette.lemon,coding_sequence_variant:i.appleCrayonPalette.spring,stop_lost:i.appleCrayonPalette.cantaloupe,"*":"#377eb8"});export{o as default};
+import{__awaiter as e}from"tslib";import t from"jquery";import i from"igv/dist/igv.esm";const s="impact",a=[{field:"type",label:"Variant Type",default:"SNV"},{field:"filter",label:"CADD Score",default:"Not reported"},{field:"is_adsp_variant",label:"ADSP Variant",default:"No"},{field:"impact",label:"Consequence Severity",default:"NONE"},{field:"consequence",label:"Consequence Type",default:"other / no predicted consequence"},{field:"is_coding",label:"Coding Variant",default:"No"}];class o extends i.TrackBase{constructor(e,t){e.hasOwnProperty("description")&&(e.hasOwnProperty("metadata")?e.metadata=Object.assign(e.metadata,{Descripton:e.description}):e.metadata={Description:e.description},delete e.description),super(e,t)}init(e){super.init(e),this.visibilityWindow=e.visibilityWindow,this.displayMode=e.displayMode||"EXPANDED",this.labelDisplayMode=e.labelDisplayMode,this.expandedVariantHeight=e.expandedVariantHeight||e.variantHeight||10,this.squishedVariantHeight=e.squishedVariantHeight||2,this.squishedCallHeight=e.squishedCallHeight||1,this.expandedCallHeight=e.expandedCallHeight||10,this.expandedVGap=void 0!==e.expandedVGap?e.expandedVGap:2,this.squishedVGap=void 0!==e.squishedVGap?e.squishedVGap:1,this.expandedGroupGap=e.expandedGroupGap||10,this.squishedGroupGap=e.squishedGroupGap||5,this.featureHeight=e.featureHeight||14,this.featureSource=i.FeatureSource(e,this.browser.genome),this.noGenotypeColor=e.noGenotypeColor||"rgb(200,180,180)",this.noCallColor=e.noCallColor||"rgb(225, 225, 225)",this.nonRefColor=e.nonRefColor||"rgb(200, 200, 215)",this.mixedColor=e.mixedColor||"rgb(200, 220, 200)",this.homrefColor=e.homrefColor||"rgb(200, 200, 200)",this.homvarColor=e.homvarColor||"rgb(17,248,254)",this.hetvarColor=e.hetvarColor||"rgb(34,12,253)",this.sortDirection="ASC",this.type=e.type||"variant",this.infoURL=e.infoURL||void 0,this.colorBy=void 0===e.colorBy?s:e.colorBy,this._initColorBy=void 0===e.colorBy?s:e.colorBy,e.colorTable&&(this.colorTables=new Map,this.colorTables.set(e.colorBy,new i.ColorTable(e.colorTable))),this._color=e.color,this.showGenotypes=void 0===e.showGenotypes||e.showGenotypes,this.variantRowCount(1)}postInit(){return e(this,void 0,void 0,function*(){return this.header=yield this.getHeader(),"dbSNP"===this.config.id?(this.visibilityWindow=1e5,this.displayMode="SQUISHED"):void 0===this.visibilityWindow&&!1!==this.config.indexed&&("function"==typeof this.featureSource.defaultVisibilityWindow?this.visibilityWindow=yield this.featureSource.defaultVisibilityWindow():this.visibilityWindow=1e6),this})}supportsWholeGenome(){return!1}get color(){return this._color}set color(e){this._color=e,this.colorBy=void 0}getHeader(){return e(this,void 0,void 0,function*(){if(!this.header){if("function"==typeof this.featureSource.getHeader){const e=yield this.featureSource.getHeader();e&&(this.callSets=e.callSets||[]),this.header=e}this.sampleNames=this.callSets?this.callSets.map(e=>e.name):[]}return this.header})}getCallsetsLength(){return this.callSets?this.callSets.length:0}getFeatures(t,i,s,a){return e(this,void 0,void 0,function*(){return void 0===this.header&&(this.header=yield this.getHeader()),this.featureSource.getFeatures({chr:t,start:i,end:s,bpPerPixel:a,visibilityWindow:this.visibilityWindow})})}hasSamples(){return this.getCallsetsLength()>0}getSamples(){return{yOffset:this.sampleYOffset,names:this.sampleNames,height:this.sampleHeight}}computePixelHeight(e){if(!e||0==e.length)return 10;const t="COLLAPSED"===this.displayMode?1:this.nVariantRows,i="SQUISHED"===this.displayMode?this.squishedVGap:this.expandedVGap,s="SQUISHED"===this.displayMode?this.squishedVariantHeight:this.expandedVariantHeight,a="SQUISHED"===this.displayMode?this.squishedCallHeight:this.expandedCallHeight;return 10+t*(s+i)+i+((!1===this.showGenotypes?0:this.getCallsetsLength()*t)+1)*(a+i)}variantRowCount(e){this.nVariantRows=e}draw(e){const{context:t,pixelWidth:s,pixelHeight:a,bpPerPixel:o,bpStart:l,pixelTop:r,features:n}=e;i.IGVGraphics.fillRect(t,0,r,s,a,{fillStyle:"rgb(255, 255, 255)"});const h="SQUISHED"===this.displayMode?this.squishedVGap:this.expandedVGap,c="COLLAPSED"===this.displayMode?1:this.nVariantRows,p="SQUISHED"===this.displayMode?this.squishedVariantHeight:this.expandedVariantHeight;this.variantBandHeight=10+c*(p+h);const d=this.callSets,u=this.getCallsetsLength();if(d&&u>0&&!1!==this.showGenotypes&&i.IGVGraphics.strokeLine(t,0,this.variantBandHeight,s,this.variantBandHeight,{strokeStyle:"rgb(224,224,224) "}),n){const e="SQUISHED"===this.displayMode?this.squishedCallHeight:this.expandedCallHeight,a="SQUISHED"===this.displayMode?this.squishedVGap:this.expandedVGap,r=l+s*o+1;for(const s of n){if(s.end<l)continue;if(s.start>r)break;const n="SQUISHED"===this.displayMode?this.squishedVariantHeight:this.expandedVariantHeight,h=10+("COLLAPSED"===this.displayMode?0:s.row*(n+a)),c=n;let p=Math.round((s.start-l)/o);const f=Math.round((s.end-l)/o);let g=Math.max(1,f-p);if(g<3?(g=3,p-=1):g>5&&(p+=1,g-=2),i.IGVGraphics.fillRect(t,p,h,g,c,{fillStyle:this.getVariantColor(s)}),s.pixelRect={x:p,y:h,w:g,h:c},u>0&&!1!==this.showGenotypes){const o="COLLAPSED"===this.displayMode?1:this.nVariantRows;this.sampleYOffset=this.variantBandHeight+a,this.sampleHeight=o*(e+a);let l=0;for(const o of d){const r=s.calls[o.id];if(r){const n="COLLAPSED"===this.displayMode?0:s.row,h=this.sampleYOffset+l*this.sampleHeight+n*(e+a);let c,d=!0,u=!0,f=!1;if(r.genotype)for(const e of r.genotype){if("."===e){f=!0;break}0!==e&&(u=!1),0===e&&(d=!1)}c=r.genotype?f?this.noCallColor:u?this.homrefColor:d?this.homvarColor:this.hetvarColor:this.noGenotypeColor,i.IGVGraphics.fillRect(t,p,h,g,e,{fillStyle:c}),o.pixelRect={x:p,y:h,w:g,h:e}}l++}}}}else console.log("No feature list")}getConsequenceValue(e){const t=e.replace(/ /g,"_");return t.includes(",")?t.split(",")[0]:t}getVariantClass(e,t){if(t.includes("dup"))return"DUP";const i=t.includes("ins"),s=t.includes("del");return i&&s?"INDEL":i?"INS":s?"DEL":e}getColorByValue(e){var t,i,s;switch(this.colorBy){case"type":return this.getVariantClass(e.variant_class_abbrev,e.display_allele);case"is_adsp_variant":return e.is_adsp_variant;case"impact":return null!==e.most_severe_consequence?null===(t=e.most_severe_consequence)||void 0===t?void 0:t.impact:"*";case"consequence":return null!==e.most_severe_consequence?this.getConsequenceValue(null===(i=e.most_severe_consequence)||void 0===i?void 0:i.conseq):"*";case"is_coding":return null!==e.most_severe_consequence?null===(s=e.most_severe_consequence)||void 0===s?void 0:s.is_coding:"*";default:return"*"}}getFilterValue(e){return"."===e||null===e?0:parseFloat(e)}getVariantColor(e){const t=e._f||e;let i;if(this.colorBy){const e="filter"===this.colorBy?this.getFilterValue(t.filter):this.getColorByValue(t.info);i=this.getVariantColorTable(this.colorBy).getColor(e),i||(i="gray")}else i=this._color?"function"==typeof this._color?this._color(t):this._color:"NONVARIANT"===t.type?this.nonRefColor:"MIXED"===t.type?this.mixedColor:this.defaultColor;return i}clickedFeatures(e,t){let i=super.clickedFeatures(e,t);const s="EXPANDED"===this.displayMode?this.expandedVGap:this.squishedVGap,a=s+("SQUISHED"===this.displayMode?this.squishedCallHeight:this.expandedCallHeight),o=e.y;if(o<=this.variantBandHeight){const e="SQUISHED"===this.displayMode?this.squishedVariantHeight:this.expandedVariantHeight,t=Math.floor((o-10)/(e+s));i=i.filter(e=>e.row===t)}else if(this.callSets){const e=this.callSets,t=o-this.variantBandHeight,s=Math.floor(t/this.sampleHeight);if(s>=0&&s<e.length){const o=Math.floor((t-s*this.sampleHeight)/a),l=i.filter(e=>e.row===o),r=e[s];i=l.map(e=>{const t=e.calls[r.id];return function(e,t){if(e.genotype){let i="";if("."===t.alternateBases)i="No Call";else{const s=t.alternateBases.split(",");for(const a of e.genotype)if(i.length>0&&(i+="|"),"."===a)i+=".";else if(0===a)i+=t.referenceBases;else{i+=s[a-1].replace("<","&lt;")}}e.genotypeName=i}}(t,e),t})}}return i}popupData(e,t){const i=this.clickedFeatures(e,t),s=e.genomicLocation,a=this.browser.genome.id,o=this.browser.sampleInformation,l=[];for(const e of i){const t=e._f||e;if(l.length>1&&l.push({html:"<hr/>"}),"function"==typeof t.popupData){const e=t.popupData(s,a);Array.prototype.push.apply(l,e)}else{const e=t;if(void 0!==e.callSetName&&l.push({name:"Name",value:e.callSetName}),e.genotypeName&&l.push({name:"Genotype",value:e.genotypeName}),void 0!==e.phaseset&&l.push({name:"Phase set",value:e.phaseset}),void 0!==e.genotypeLikelihood&&l.push({name:"genotypeLikelihood",value:e.genotypeLikelihood.toString()}),o){const t=o.getAttributes(e.callSetName);t&&Object.keys(t).forEach(function(e){let i=e.replace(/([A-Z])/g," $1");i=i.charAt(0).toUpperCase()+i.slice(1),l.push({name:i,value:t[e]})})}const i=this.getVariantColor(e);if(this.infoURL){const t=this.infoURL+"/variant/"+e.id;l.push({name:"Variant:",html:`<a target="_blank" href="${t}">${e.info.display_id}</a>`,title:"Learn more about this variant: "+e.info.display_id})}else l.push({name:"Variant:",value:e.info.display_id});if(null!==e.info.ref_snp_id&&l.push({name:"Ref SNP ID:",value:e.info.ref_snp_id}),l.push({name:"Location:",value:e.chr+":"+e.info.location}),l.push({name:"Allele:",value:e.info.display_allele}),"type"===this.colorBy?l.push({name:"Class:",value:this.getVariantClass(e.info.variant_class_abbrev,e.info.display_allele),color:i}):l.push({name:"Class:",value:this.getVariantClass(e.info.variant_class_abbrev,e.info.display_allele)}),"is_adsp_variant"===this.colorBy?l.push({name:"ADSP Variant?",value:null===e.info.is_adsp_variant?"No":"Yes",color:i}):l.push({name:"ADSP Variant?",value:null===e.info.is_adsp_variant?"No":"Yes"}),this.getFilterValue(e.filter)>0&&("filter"===this.colorBy?l.push({name:"CADD (PHRED):",value:e.filter,color:i}):l.push({name:"CADD (PHRED):",value:e.filter})),null!==e.info.most_severe_consequence){const t=e.info.most_severe_consequence;if("consequence"===this.colorBy?l.push({name:"Consequence:",value:t.conseq,color:i}):l.push({name:"Consequence:",value:t.conseq}),"impact"===this.colorBy?l.push({name:"Impact:",value:t.impact,color:i}):l.push({name:"Impact:",value:t.impact}),"is_coding"===this.colorBy?l.push({name:"Is Coding?",value:null===t.is_coding?"No":t.is_coding?"Yes":"No",color:i}):l.push({name:"Is Coding?",value:null===t.is_coding?"No":t.is_coding?"Yes":"No"}),null!==t.impacted_gene)if(this.infoURL){const e=this.infoURL+"/gene/"+t.impacted_gene;l.push({name:"Impacted Gene:",html:`<a target="_blank" href="${e}">${t.impacted_gene_symbol}</a>`,title:"Learn more about gene: "+t.impacted_gene_symbol})}else l.push({name:"Impacted Gene:",value:t.impacted_gene_symbol})}}}return l}menuItemList(){const e=[];e.push("<hr/>");const s=t('<div class="igv-track-menu-category igv-track-menu-border-top">');s.text("Color by:"),e.push({name:void 0,object:s,click:void 0,init:void 0}),a.forEach(t=>{const i=this.colorBy===t.field;"is_adsp_variant"===t.field&&this.config.id.includes("ADSP")||e.push(this.colorByCB({key:t.field,label:t.label},i))}),e.push(this.colorByCB({key:void 0,label:"None"},void 0===this.colorBy)),e.push("<hr/>"),this.getCallsetsLength()>0&&(e.push({object:t('<div class="igv-track-menu-border-top">')}),e.push({object:t(i.createCheckbox("Show Genotypes",this.showGenotypes)),click:()=>{this.showGenotypes=!this.showGenotypes,this.trackView.checkContentHeight(),this.trackView.repaintViews()}})),e.push({object:t('<div class="igv-track-menu-border-top">')});const o={COLLAPSED:"Collapse",SQUISHED:"Squish",EXPANDED:"Expand"};for(const s of Object.keys(o))e.push({object:t(i.createCheckbox(o[s],s===this.displayMode)),click:()=>{this.displayMode=s,this.trackView.checkContentHeight(),this.trackView.repaintViews()}});return this.browser.circularView&&!0===this.browser.circularViewVisible&&(e.push("<hr>"),e.push({label:"Add SVs to circular view",click:()=>{const e=[];for(const t of this.trackView.viewports){const i=t.referenceFrame;for(const s of t.getCachedFeatures())s.end>=i.start&&s.start<=i.end&&e.push(s)}const t=i.makeVCFChords(e),s=i.IGVColor.addAlpha(this._color||this.defaultColor,.5);this.browser.circularView.addChords(t,{track:this.name,color:s})}})),e}contextMenuItemList(e){if(this.browser.circularView&&!0===this.browser.circularViewVisible){const t=e.viewport,s=[];return s.push({label:"Add SVs to Circular View",click:()=>{const e=t.referenceFrame,s="all"===e.chr?this.featureSource.getAllFeatures():this.featureSource.featureCache.queryFeatures(e.chr,e.start,e.end),a=i.makeVCFChords(s),o=i.IGVColor.addAlpha(this._color||this.defaultColor,.5);this.browser.circularView.addChords(a,{track:this.name,color:o})}}),s.push("<hr/>"),s}}description(){const e=(e,t)=>`<div class="igv-track-label-popup-shim"><b>${e}: </b>${t}</div>`,t=(e,t)=>`<div class="igv-track-label-popup-shim"><i class="fa fa-square" style="color:${t}"></i> ${e}</div>`;let i='<div class="igv-track-label-popup">';if(i+=e("Track",this.name),this.config&&this.config.metadata)for(const t of Object.keys(this.config.metadata)){i+=e(t,this.config.metadata[t])}if(i+="</div>",this.colorBy){i+='<hr><div class="igv-track-label-popup">';const s=a.filter(e=>e.field==this.colorBy)[0];if(i+=e("Legend",s.label),i+="<br>","filter"===this.colorBy){const e=this.getVariantColorTable(this.colorBy);for(const[s,a]of e.colors.entries()){const o=e.thresholds[s];i+=t(0===o?"N/A":o,a)}}else{const e=this.getVariantColorTable(this.colorBy).colorTable;for(const[a,o]of Object.entries(e))i+=t(a.includes("*")?s.default:"true"===a?"Yes":a.replace("_"," "),o)}i+="</div>"}return i}colorByCB(e,s){return{name:void 0,object:t(i.createCheckbox(e.label,s)),click:()=>{e.key===this.colorBy?(this.colorBy=void 0,delete this.config.colorBy,this.trackView.repaintViews()):(this.colorBy=e.key,this.config.colorBy=e.key,this.trackView.repaintViews())},init:void 0}}getState(){const e=super.getState();return this._color&&"function"!=typeof this._color&&(e.color=this._color),e}getVariantColorTable(e){if(this.colorTables||(this.colorTables=new Map),!this.colorTables.has(e)){let t;switch(e){case"type":t=r;break;case"consequence":t=c;break;case"is_adsp_variant":case"is_coding":t=h;break;case"impact":t=n;break;case"filter":t=l;break;default:t=new i.PaletteColorTable("Set1")}this.colorTables.set(e,t)}return this.colorTables.get(e)}}const l=new i.BinnedColorScale({thresholds:[0,1,10,20,30,40,50],colors:["#45515c","#440d53","#443983","#32678d","#23908c","#37b779","#8fd744"]}),r=new i.ColorTable({DEL:"#ff2101",INS:"#f59300",DUP:"#028401",INV:"#008688",CNV:"#8931ff",INDEL:"#891100","*":"#45515c"}),n=new i.ColorTable({HIGH:"#ff00ff",MODERATE:"#f59300",LOW:"#008000",MODIFIER:"#377eb8","*":"#45515c"}),h=new i.ColorTable({true:"#e41a1c","*":"#45515c"}),c=new i.ColorTable({splice_acceptor_variant:i.appleCrayonPalette.salmon,start_lost:i.appleCrayonPalette.honeydew,splice_region_variant:i.appleCrayonPalette.fern,prime_UTR_variant:i.appleCrayonPalette.clover,splice_donor_variant:i.appleCrayonPalette.moss,inframe_insertion:i.appleCrayonPalette.teal,splice_donor_region_variant:i.appleCrayonPalette.midnight,non_coding_transcript_exon_variant:i.appleCrayonPalette.eggplant,stop_gained:i.appleCrayonPalette.plum,inframe_deletion:i.appleCrayonPalette.maroon,stop_retained_variant:i.appleCrayonPalette.aqua,intron_variant:i.appleCrayonPalette.mocha,missense_variant:i.appleCrayonPalette.maraschino,synonymous_variant:i.appleCrayonPalette.tangerine,intergenic_variant:i.appleCrayonPalette.ocean,frameshift_variant:i.appleCrayonPalette.bubblegum,protein_altering_variant:i.appleCrayonPalette.lemon,coding_sequence_variant:i.appleCrayonPalette.spring,stop_lost:i.appleCrayonPalette.cantaloupe,"*":"#377eb8"});export{o as default};
 //# sourceMappingURL=VariantServiceTrack.js.map

package/dist/tracks/VariantServiceTrack.js.map

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package/dist/utils/browser.js

@@ -1,2 +1,2 @@
-import{__awaiter as i,__asyncValues as r}from"tslib";import{GENOMICSDB_ROOT as o,ALWAYS_ON_TRACKS as e}from"../config/_constants.js";import{getViewTrackIdentifier as n}from"./views.js";import{resolveServiceTrackReader as t}from"./track_config.js";const d=(i,r=e)=>{var o;return(null!==(o=null==i?void 0:i.trackViews)&&void 0!==o?o:[]).map(i=>n(i)).filter(i=>!r.includes(i))},c=(i,r)=>{var o;const e=(null!==(o=null==i?void 0:i.trackViews)&&void 0!==o?o:[]).filter(i=>n(i)===r);i.removeTrack(e[0].track)},l=(r,e)=>i(void 0,void 0,void 0,function*(){if("format"in e&&null!=e.format.match("^bed\\d{1,2}\\+\\d+$")){const{default:i}=yield import("../decoders/bedDecoder.js");e.decode=i}if(e.url.includes("$CHR")){const{default:i}=yield import("../readers/ShardedBedReader.js");e.reader=new i(e,r.genome)}e.type.includes("_service")&&(e.reader=yield t({endpoint:e.url,track:e.id},e.type)),e.infoURL&&"/record"===e.infoURL&&(e.infoURL=`${o}/record`),yield r.loadTrack(e)}),a=(o,e)=>i(void 0,void 0,void 0,function*(){var i,n,t;try{for(var d,c=!0,a=r(e.map(i=>l(o,i)));!(i=(d=yield a.next()).done);c=!0){d.value,c=!1}}catch(i){n={error:i}}finally{try{c||i||!(t=a.return)||(yield t.call(a))}finally{if(n)throw n.error}}});function f(r,o,e){return i(this,void 0,void 0,function*(){const i=o.filter(i=>!e.includes(i.id));return i.length>0?(yield a(r,i),i.map(i=>i.id)):[]})}function s(r,o,e){return i(this,void 0,void 0,function*(){const i=e.filter(i=>!o.some(r=>r.id===i));for(const o of i)c(r,o);return i})}function u(r,o){return i(this,void 0,void 0,function*(){const i=d(r,r.config.alwaysOnTracks);yield f(r,o,i),yield s(r,o,i)})}export{d as getLoadedTracks,f as handleAddTracksToBrowser,s as handleRemoveTracksFromBrowser,u as handleUpdateBrowserTracks,l as loadTrack,a as loadTracks,c as removeTrackById};
+import{__awaiter as i,__asyncValues as o}from"tslib";import{ALWAYS_ON_TRACKS as r,QTL_VISIBILITY_WINDOW as e,GENOMICSDB_ROOT as n}from"../config/_constants.js";import{getViewTrackIdentifier as d}from"./views.js";import{resolveServiceTrackReader as t}from"./track_config.js";const l=(i,o=r)=>{var e;return(null!==(e=null==i?void 0:i.trackViews)&&void 0!==e?e:[]).map(i=>d(i)).filter(i=>!o.includes(i))},c=(i,o)=>{var r;const e=(null!==(r=null==i?void 0:i.trackViews)&&void 0!==r?r:[]).filter(i=>d(i)===o);i.removeTrack(e[0].track)},a=(i,o=r)=>{var e;(null!==(e=null==i?void 0:i.trackViews)&&void 0!==e?e:[]).forEach(r=>{const e=d(r);o.includes(e)||i.removeTrack(r.track)})},s=(o,r)=>i(void 0,void 0,void 0,function*(){var i,d;if("format"in r&&null!=(null===(i=r.format)||void 0===i?void 0:i.match("^bed\\d{1,2}\\+\\d+$"))){const{default:i}=yield import("../decoders/bedDecoder.js");r.decode=i,r.visibilityWindow=e,r.supportsWholeGenome=!1}if(r.url.includes("$CHR")){const{default:i}=yield import("../readers/ShardedBedReader.js");r.reader=new i(r,o.genome)}(null===(d=r.type)||void 0===d?void 0:d.includes("_service"))&&(r.reader=yield t({endpoint:r.url,track:r.id},r.type)),r.infoURL&&"/record"===r.infoURL&&(r.infoURL=`${n}/record`),yield o.loadTrack(r)}),f=(r,e)=>i(void 0,void 0,void 0,function*(){var i,n,d;try{for(var t,l=!0,c=o(e.map(i=>s(r,i)));!(i=(t=yield c.next()).done);l=!0){t.value,l=!1}}catch(i){n={error:i}}finally{try{l||i||!(d=c.return)||(yield d.call(c))}finally{if(n)throw n.error}}});function u(o,r,e){return i(this,void 0,void 0,function*(){const i=r.filter(i=>!e.includes(i.id));return i.length>0?(yield f(o,i),i.map(i=>i.id)):[]})}function v(o,r,e){return i(this,void 0,void 0,function*(){const i=e.filter(i=>!r.some(o=>o.id===i));for(const r of i)c(o,r);return i})}function m(o,r){return i(this,void 0,void 0,function*(){const i=l(o,o.config.alwaysOnTracks);yield u(o,r,i),yield v(o,r,i)})}export{a as clearTrackView,l as getLoadedTracks,u as handleAddTracksToBrowser,v as handleRemoveTracksFromBrowser,m as handleUpdateBrowserTracks,s as loadTrack,f as loadTracks,c as removeTrackById};
 //# sourceMappingURL=browser.js.map

package/dist/utils/browser.js.map

@@ -1 +1 @@
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package/package.json

@@ -1,6 +1,6 @@
 {
     "name": "@niagads/igv",
-    "version": "0.2.0",
+    "version": "0.2.1",
     "description": "NIAGADS IGV Browser Component",
     "repository": {
         "type": "git",
@@ -11,9 +11,9 @@
         "build": "rollup -c"
     },
     "dependencies": {
-        "@niagads/common": "^0.2.0",
-        "@niagads/table": "^0.2.0",
-        "@niagads/ui": "^0.2.0",
+        "@niagads/common": "^0.2.1",
+        "@niagads/table": "^0.2.1",
+        "@niagads/ui": "^0.2.1",
         "igv": "github:NIAGADS/igv.js#NIAGADS-01102025",
         "jquery": "^3.7.1",
         "tslib": "^2"
@@ -45,5 +45,5 @@
             "types": "./dist/index.d.ts"
         }
     },
-    "gitHead": "c5de63bf4a67393a68753f8f7c551fc2d1bec9f4"
+    "gitHead": "1b4b46ea64e779b861797e1a25523e1020e41d93"
 }